Use of HGMA-targeted phosphorothioate DNA aptamers to suppress carcinogenic activity and increase sensitivity to chemotherapy agents in human cancer cells

ABSTRACT

Elevated high mobility group A (HMGA) protein expression in human cancer cells, and especially human pancreatic cancer cells, is correlated with resistance to the chemotherapy agent gemcitabine. The present invention uses HMGA-targeted AT-rich phosphorothioate DNA (AT-sDNA) aptamers to suppress HMGA carcinogenic activity. Cell growth of human pancreatic cancer cells (AsPC-1 and Miapaca-2) transfected with AT-sDNA were monitored after treatment with gemcitabine. Significant increases in cell death in AT-sDNA transfected cells compared to non AT-rich sDNA treated cells were observed in both cell lines. The data indicates the potential use of HMGA targeted DNA aptamers to enhance chemotherapy efficacy in human cancer treatment, and in particular human pancreatic cancer treatment.

CROSS REFERENCE TO RELATED APPLICATIONS

This application claims the benefit of U.S. provisional patentapplication Ser. No. 61/706,228 entitled “Use of HGMA-targetedphosphorothioate DNA aptamers to suppress carcinogenic activity andincrease sensitivity to gemcitabine chemotherapy in human pancreaticcancer cells,” filed Sep. 27, 2012, and incorporated herein by referencein its entirety.

REFERENCE TO GOVERNMENT SUPPORT

The invention was developed at least in part with the support of NIHgrant number 1R15CA152985. The government may have certain rights in theinvention.

FIELD OF THE INVENTION

The present invention relates to the use of HMGA-targeted AT-richphosphorothioate DNA (AT-sDNA) aptamers to suppress HMGA carcinogenicactivity in human cancer cells and to increase the effectiveness ofchemotherapy agents.

BACKGROUND OF THE INVENTION

Elevated levels of high-mobility group A (HMGA) protein expression havebeen reported in almost every type of human cancer, including colorectalcancer, pancreatic cancer, and breast cancer. There are two forms ofHMGA proteins, HMGA1 and HMGA2, which are encoded from two differentgenes. Both forms of HMGA are non-histone chromatin architecturaltranscription factors found broadly in eukaryotes. HMGA proteins areexpressed at high levels in embryonic tissues during early developmentand at very low levels in normal differentiated somatic adult cells.Regulation of gene expression is a primary function of HMGA in thesecells and HMGA proteins are involved in both positive and negativeregulation of genes responsible for apoptosis, cell proliferation,immune response and DNA repair. Overexpression of HMGA has been shown toincrease cell proliferation contributing to tumor growth.

In addition, it has been shown that HMGA1 interacts with the p53 tumorsuppressor protein and inhibits its apoptotic activity. It has also beenshown that high expression levels of HMGA1 are responsible forchemotherapy resistance in pancreatic cancer cell lines and thatsuppression of HMGA1 expression by siRNA restored the cells sensitivityto gemcitabine. HMGA2 is responsible for maintaining Ras-inducedepithelial-mesenchymal transition that promotes tissue invasion andmetastasis. Down regulation of overexpressed HMGA2 has been shown toinhibit cell proliferation in human pancreatic cancer cell lines. Whilethe precise role that HMGA plays in cancer is not yet completelyunderstood, HMGA has been suggested as a potential biomarker for tumorprogression and is a drug target for cancer therapy development.

An early structural study showed that HMGA does not adopt a conventionalprotein structure composed of a helices or β sheets but rather binds inthe minor groove of AT-rich double-stranded DNA through crescent-shapedDNA binding motifs referred to as “AT-hooks.” In contrast to classicaltranscription factors that bind specific DNA sequences, HMGA acts as anarchitectural transcription factor that binds a specific type of DNAstructure, i.e. the minor groove of A:T tract DNA. Due to this uniqueDNA binding property of HMGA, several cancer therapy drugs, such asFR900482 and FL317, have been designed as competitive HMGA1 inhibitorsthat bind to the minor groove of AT-rich DNA. These drugs however, haveshown high toxicity in humans. Recently, it has been shown thatSpiegelmer NOX-A50 is a potent inhibitor of HMGA1 activity and proposedthe use of artificial HMGA1 substrates that block HMGA1 binding to itsnatural DNA substrate. In principle, decreasing all HMGA proteinactivity could result in inhibition of unwanted cell proliferation andreestablishment of apoptosis, reducing cancer progression.

Nucleic acid ligands designed or selected to inhibit the activity ofpathogenic proteins are referred to as aptamers or “decoys”. Nucleicacid aptamers contain variable sequences and/or modified chemicalstructures to facilitate binding to their protein targets with highspecificity and an equal to, or higher, affinity compared to theirunmodified oligomer counterparts. They are widely studied forbiotechnological and therapeutic applications because they have littleor no immunogenicity compared to antibodies and several applicationshave been reported. For example, one study has shown that overexpressionof a 60-nucleotide RNA decoy used as a antiviral treatment showedinhibition of Tat-mediated HIV replication in vitro by 90%. In anotherstudy, a 2′-fluoropyrimidine RNA was designed as a vascular endothelialgrowth factor inhibitor that reduced lung metastasis in mice. A DNAaptamer targeting transcription factor E2F, which is essential incellular proliferation regulation, was shown to decrease cellproliferation in vascular smooth muscle cells.

In addition to engineered specificity, an important property of DNAaptamers is that they are sometimes designed to be resistant toendogenous nuclease activity in vivo. For example, both phosphorothioateDNA (sDNA), which contains sulfur substituted for one oxygen atom in thephosphodiester backbone, and phosphorodithioate DNA, which containssulfur substitution of two oxygen atoms in the phosphodiester backbone,have been shown to have shown increased resistance to nuclease S1 andDeoxyribonuclease I (DNase I) activity as the number of sulfursubstitutions increases.

Since down regulation of both HMGA1 and HMGA2 proteins contributes tothe inhibition of tumor growth, the strategy of targeting both HMGA1 andHMGA2 may result in a potentially more potent therapeutic strategy thantargeted inhibition of either protein alone. Therefore, there is a needfor nuclease resistant DNA aptamers that both inhibit pancreatic cancertumor growth and increase the sensitivity of pancreatic cancer cells tochemotherapy by down regulation of both HMGA1 and HMGA2 proteins and areresistant to endogenous nuclease attack.

SUMMARY OF THE INVENTION

The present invention is generally directed phosphorothioate substitutedDNA aptamers (sDNA aptamer(s)) active against HMGA proteins that containmultiple HMGA AT-hook binding sites (AT-sDNA) to compete for HMGAprotein binding to genomic DNA and directly inhibit HMGA proteinactivity in cancer cells. Since both HMGA1 and HMGA2 bind AT-rich DNA,the sDNA aptamer is intended to inhibit the activity of both forms ofHMGA. The sDNA aptamer may be transfected into human cancer cellsincluding, in some embodiments, pancreatic adenocarcinoma cells.

In some embodiments, the present invention may be a sDNA aptamer forsuppressing the activity of HMGA proteins in human cancer cells. In someembodiments, the sDNA aptamer of the present invention suppresses theactivity of HMGA proteins in human pancreatic cancer cells.

In some embodiments, the sDNA Aptamer may have a length of from about 7to about 30 base pairs and a nucleotide sequence comprising from about 5to about 18 adenine or thymine nucleotides. In some embodiments, thelength of the sDNA aptamer is from about 17 to about 30 base pairs. Insome embodiments, the length of the sDNA aptamer is from about 20 toabout 30 base pairs. In some embodiments, the length of the sDNA aptameris from about 17 to about 30 base pairs. In some embodiments, nucleotidesequence comprises a sequence of from about 15 to about 18 adenine orthymine nucleotides. In some embodiments, the sDNA aptamer has asequence of 18 adenine or thymine nucleotides. In some embodiments, thesegment of adenine or thymine nucleotides in said nucleotide sequence isconsecutive. In some embodiments, the segment of adenine or thyminenucleotides in said nucleotide sequence is alternating or randomlymixed. In some embodiments, the segment of adenine or thyminenucleotides in said nucleotide sequence may consist of a total of threesegments of 5-6 consecutive adenine or thymine or mixed adenine andthymine residues with each segment spaced by 1-3 guanine or cytosineresidues. In some embodiments, the sDNA aptamer may have the sequence5′-G*G*G*A*A*A*A*A*A*T*T*T*T-*T*T*A*A*A*A*A*A*C*C*C-3′ (SEQ ID NO: 1)wherein the “*” are phosphorothioate linkages. In some embodiments, theaptamer sequence is self-complementary. In some embodiments, the aptamersequence is not self-complementary, requiring that two distinctsequences must be synthesized and annealed.

In some embodiments, the sDNA aptamer may inhibit HMGA protein activityin human pancreatic adenocarcinoma cells and may increase sensitivity ofhuman pancreatic adenocarcinoma cells to gemcitabine, which is used inthe treatment of various human cancers including non-small cell lungcancer, pancreatic cancer, bladder cancer and breast cancer. The sDNAaptamer may also rescue cellular apoptosis induced by gemcitabinetreatment and may prevent excess HMGA from binding to chromosomal DNAtranscription factors and other proteins involved in regulatingapoptosis and cell proliferation in tumor progression.

In some embodiments, the sDNA aptamer may have substantial resistance tothe activity of endogenous nucleases, such as Deoxyribonuclease I.

One method of practicing the claimed invention may include a methodincreasing sensitivity to chemotherapy agents in human cancer cellscomprising: (i) administering a therapeutically effective amount of achemotherapy agent to a patient; and (ii) administering atherapeutically effective amount of a sDNA aptamer having a length offrom about 7 to about 30 base pairs and a nucleotide sequence comprisingfrom about 5 to about 18 adenine or thymine nucleotides to the patientwhereby the sensitivity of the human cancer cells to the chemotherapyagent is increased. In some embodiments, the human cancer cells arehuman pancreatic cancer cells. In some embodiments, the chemotherapyagent is gemcitabine.

Another method for practicing the invention may include a method ofsuppressing the activity of High Mobility Group A (HMGA) proteins inhuman cancer cells comprising: (i) administering a therapeuticallyeffective amount of a chemotherapy agent to a patient; and (ii)administering a therapeutically significant amount of the sDNA aptamerhaving a length of from about 7 to about 30 base pairs and a nucleotidesequence comprising from about 5 to about 18 adenine or thyminenucleotides to the patient whereby the activity of High Mobility Group A(HMGA) proteins in the human cancer cells is reduced. In someembodiments, the human cancer cells are human pancreatic cancer cells.In some embodiments, the chemotherapy agent is gemcitabine.

Yet another method for practicing the invention may include a method fortreating human pancreatic adenocarcinoma comprising: (i) administering atherapeutically effective amount of gemcitabine, or a pharmaceuticallyacceptable salt thereof, to a patient; and (ii) administering atherapeutically significant amount of the phosphorothioate substitutedsDNA aptamer having a length of from about 7 to about 30 base pairs anda nucleotide sequence comprising from about 5 to about 18 adenine orthymine nucleotides to the patient whereby the number of the pancreaticadenocarcinoma cells in the patient is reduced. In some embodiments, thepancreatic adenocarcinoma cells in the patient are reduced in an amountgreater than the reduction of the number of the pancreaticadenocarcinoma cells achieved through administration of saidgemcitabine, or a pharmaceutically acceptable salt thereof, to saidpatient without administering the phosphorothioate substituted sDNAaptamer.

BRIEF DESCRIPTION OF THE DRAWINGS

For a more complete understanding of the features and advantages of thepresent invention, reference is now made to the detailed description ofthe invention along with the accompanying figures in which:

FIG. 1A is an image from an electrophoretic mobility shift assay (EMSA)of an HMGA1 competitive binding assay using sDNA and unmodified DNA.Lanes 1 and 9, ATf10 and ATs10 respectively, are controls that do notcontain HMGA1. The ratios between HMGA1 and ATf10 were kept constant at1.5 (excess HMGA1, lane 2) and an increased amount of ATs10 was added tothe reactions in lanes 3 to 8.

FIG. 1B is an image from an EMSA of HMGA1 competitive binding assayusing CG10 and Mix10 DNA. Lanes 2-4 contain equal amounts of ATf10 andCG10 or Mix10. ATf10 DNA: HMGA1 in lanes 2-4 was kept constant at a 1:1ratio. The arrow indicates free (unshifted) DNA and the * indicates thecomplex (shifted bands) with ATf10 DNA. The images were taken at 495 nmusing a BIO-RAD VersaDoc Imaging System Model 3000 in order to visualizethe ATf10.

FIG. 2 is an image from a nuclease resistance assay for sDNA with DNaseI. 0.25 nmol of A) AT15, B) As10Ts10, C) As10Ts20 and D) As20Ts20 wereincubated for 0 to 12 hours and run on a 7% native polyacrylamide gel.The gel was stained with ethidium bromide and visualized using anAlphaImager.

FIGS. 3A and 4A are images and FIGS. 3B and 4B are corresponding graphsshowing the results of a western blot analysis of HMGA1 (FIGS. 3A and3B) and HMGA2 (FIGS. 4A and 4B) expression levels in pancreatic cancercell lines. Nuclear extracts of AsPC-1, Miapaca-2, and Panc-1 cell lineswere run on a 4-12% gradient gel. In each lane, 25 μg of total nuclearprotein was loaded.

FIG. 5A contains images and a FIG. 5B is a corresponding graph showingthe results of an assay in which 15 μg of total nuclear protein wasloaded in each lane after AsPC-1 cells treated with 100 nM gemcitabinefor 48 hours and transfected with 0.5 μg of CG-sDNA, or AT-sDNA in sixwell plates for 48 hours. The control is nuclear extract from untreatedcells. Triplicates of each sample were run on the gel and analyzed withthe Alpha Imager. The relative HMGA1 densities were obtained by dividingHMGA1density by TBP density. The values were analyzed pair wise using astudent t-test, with p values <0.05 considered a significant change(*p<0.05). TATA binding protein (TBP) was used as a loading control.

FIGS. 6A and 6B reports the results of a cell viability assay done aftersDNA transfection. Miapaca-2 (FIG. 6A) and AsPC-1 (FIG. 6B) cells weretransfected with two doses of sDNA. Cells were fixed 48 and 96 hoursafter transfection and analyzed with the crystal violet assay asdescribed in the methods. The absorbance was measured at 570 nm inquadruplicate. All data from control cells were combined and averaged.The values were analyzed pair wise with TC using a student t-test, withp values <0.05 considered a significant change (*p<0.05, **p<0.01).

FIGS. 8A-8D are a series of graphs reporting IC₅₀ determinations forvarious doses of sDNA transfection with gemcitabine treatment forAsPC-1: 0.1 μg transfection (FIG. 8A) and 0.25 μg transfection (FIG.8B), and for Miapaca-2: 0.1 μg transfection (FIG. 8C) and 0.25 μgtransfection (FIG. 8D).

FIGS. 10A-D, 11A-D, and 12A-C are a series of graphs reporting a dosedependent response to gemcitabine treatment after sDNA transfection at96 hours. FIG. 10 is a series of graphs reporting a dose dependentresponse to gemcitabine treatment after sDNA transfection in Miapaca-2at 96 hours. The Miapaca-2 cells were transfected with 0.1 μg of TC-sDNA(FIG. 10A), Mix-sDNA (FIG. 10A), CG-sDNA (FIG. 10C), and AT-sDNA (FIG.10D). FIGS. 11A-D and 12A-C are graphs reporting dose dependentresponses to gemcitabine treatment in AsPC-1 cells at 96 hours at 0.1 μg(FIGS. 11A-D) and 0.25 μg (FIGS. 11A-D) transfection per 5×10⁴-1×10⁵cancer cells. The AsPC-1 cells were transfected with 0.1 μg of TC-sDNA(FIG. 11A), Mix-sDNA (FIG. 11A), CG-sDNA (FIG. 11C), and AT-sDNA (FIG.11D) and with 0.25 μg of TC-sDNA (FIG. 12A), CG-sDNA (FIG. 12B), andAT-sDNA (FIG. 12C). The data was normalized with the 0 nM gemcitabinetreated cells and the resulting value defined as a value of 1. Thevalues were analyzed in pairs using a student t-test, with p values<0.05 considered a significant change (*p<0.05, **p<0.01, ***p<0.001).

FIGS. 7A and 7B are graphs showing dose dependant response to sDNAtransfection in AsPC-1 at 48 (FIG. 7A) and 96 hours (FIG. 7B). Cellswere transfected with 0.025 μg, 0.1 μg, 0.25 μg, and 1.0 μg, of CG-sDNA,and AT-sDNA. Data was normalized with the 0 nM gemcitabine treated cellsdefined as a value of 1. The values were analyzed pair wise using astudent t-test, with p values <0.05 considered a significant change(*p<0.05).

FIGS. 9A and 9B are graphs showing dose dependant response togemcitabine treatment after sDNA transfection in Miapaca-2 (FIG. 9A) andAspC-1 (FIG. 9B) at 48 hours. Cells were transfected with 0.1 ug ofMix-sDNA. Data was normalized with the 0 nM gemcitabine treated cellsdefined as a value of 1. The values were analyzed pair wise using astudent t-test, with p values <0.05 considered a significant change(*p<0.05).

DETAILED DESCRIPTION OF ILLUSTRATIVE EMBODIMENTS

While the making and using of various embodiments of the presentinvention are discussed below, it should be appreciated that the presentinvention provides many applicable inventive concepts that can beembodied in a variety of specific contexts. The specific embodimentsdiscussed herein are merely illustrative of specific ways to make anduse the invention and do not delimit the scope of the invention.

The abbreviations used herein should be well understood by those ofordinary skill in the art, but are set forth here for clarity.Accordingly, as used herein, “ATfDNA” means fluorescence labeled DNA;“AT-sDNA” means AT-rich phosphorothioate DNA; “CG-sDNA” means CG-richphosphorothioate DNA; “DMEM” means Dulbecco's Modified Eagle Medium;“DNase I” means Deoxyribonuclease I; “EMSA” means electrophoreticmobility shift assay; “FBS” means fetal bovine serum; “HMGA” means highmobility group A; “IC₅₀” means half maximal inhibitory concentration;“IPTG” means isopropyl β-D-1-thiogalactopyranoside; “Mix-sDNA” meansrandom sequence phosphorothioate DNA; “sDNA” means phosphorothioate DNA;“TAE” means Tris base, acetic acid and EDTA buffer; “cDNA” meanscomplementary DNA; “PVDF” means polyvinlidene fluoride; “PBST” meansphosphate buffered saline with Tween 20; “BSA” means bovine serumalbumin; “RPIM” means Roswell Park Memorial Institute medium; “SDS-PAGE”means sodium dodecyl sulfate polyacrylamide gel electrophoresis; and“TPB” means TATA binding protein.

Unless otherwise specified, compounds referenced herein are“commercially available” and may be obtained from standard commercialsources including, without limitation, Acros Organics (Pittsburgh Pa.),Aldrich Chemical (Milwaukee Wis., including Sigma Chemical and Fluka),Apin Chemicals Ltd. (Milton Park U.K.), Avocado Research (LancashireU.K.), SDH Inc. (Toronto, Canada), Bionet (Cornwall, U.K.), ChemserviceInc. (West Chester Pa.), Crescent Chemical Co. (Hauppauge N.Y.), EastmanOrganic Chemicals, Eastman Kodak Company (Rochester N.Y.), FisherScientific Co. (Pittsburgh Pa.), Fisons Chemicals (Leicestershire U.K.),Frontier Scientific (Logan Utah), ICN Biomedicals, Inc. (Costa MesaCalif.), Key Organics (Cornwall U.K.), Lancaster Synthesis (WindhamN.H.), Maybridge Chemical Co. Ltd. (Cornwall U.K.), Parish Chemical Co.(Orem Utah), Pfaltz & Bauer, Inc. (Waterbury Conn.), Polyorganix(Houston Tex.), Pierce Chemical Co. (Rockford Ill.), Riedel de Haen AG(Hannover, Germany), Spectrum Quality Product, Inc. (New Brunswick,N.J.), TCI America (Portland Oreg.), Trans World Chemicals, Inc.(Rockville Md.), Wako Chemicals USA, Inc. (Richmond Va.), Novabiochemand Argonaut Technology.

As set forth above, elevated levels of high-mobility group A (HMGA)protein expression have been reported in almost every type of humancancer. Overexpression of HMGA has been shown to increase cellproliferation contributing to tumor growth and HMGA1 interacts with thep53 tumor suppressor protein and inhibits its apoptotic activity. It hasalso been shown that high expression levels of HMGA1 are responsible forchemotherapy resistance in pancreatic cancer cell lines and thatsuppression of HMGA1 expression by siRNA restored the cells sensitivityto chemotherapy agents like gemcitabine. HMGA2 is responsible formaintaining Ras-induced epithelial-mesenchymal transition that promotestissue invasion and metastasis. Down regulation of overexpressed HMGA2has been shown to inhibit cell proliferation in human pancreatic cancercell lines.

Broadly speaking, the present invention is directed to use of highmobility group A (HMGA)-targeted AT-rich phosphorothioate DNA (AT-sDNA)aptamers as essentially a “decoy” to bind with and limit the activity ofHMGA proteins, particularly in cancer cells. HMGA proteins containmultiple AT-hook binding sites, and will bind with certain areas of theAT-sDNA aptamers of the present invention rather than with genomic DNAor other receptors, as it would but for the presence of the AT-sDNAaptamers, In this way, the AT-sDNA aptamers of the present inventiondirectly inhibit HMGA protein activity in cancer and other cells wherethe HMGA proteins are being overexpressed. Since both HMGA1 and HMGA2bind AT-rich DNA, the disclosed sDNA aptamer is intended to inhibit theactivity of both forms of HMGA, which may result in potentially morepotent therapeutic strategies than inhibiting the activity of eitherprotein alone. HGMA-targeted phosphorothiate DNA aptamers increasesensitivity to gemcitabine chemotherapy in human pancreatic cancer celllines. See also, Watanabe et al. Cancer Letters 315 (2012) 18-27, thedisclosure of which is hereby incorporated by reference in its entirety.

The AT-sDNA aptamers of the present invention are an adenine and thyminerich phosphorothioate substituted oligonucleotide sequence of from about7 to about 30 nucleotides in length. In some embodiments, the AT-sDNAaptamer may be from about 15 to about 30 nucleotides in length. In someembodiments, the AT-sDNA aptamer may be from about 20 to about 30nucleotides in length.

Each HGMA protein is believed to have three AT-hook binding sites andthe AT-sDNA aptamers of the present invention may bind to one, two orall three of the sites, depending upon the affinity of the particularAT-sDNA aptamer for the protein. See Watanabe et al., Characterizationof the Stoichiometry of HMGA1/DNA Complexes, The Open BiochemistryJournal, 2013, 7, 73-81, the disclosure of which is incorporated hereinby reference in its entirety. It is believed that each one of theseAT-hook binding sites is configured to receive a segment of AT-sDNAaptamer having a sequence of 5 or 6 adenine or thymine nucleotides. Aswill be appreciated, AT-sDNA aptamers having the highest affinity forthe HMGA proteins will have three sequences of 5 or 6 adenine or thyminenucleotides for each AT-hook binding site on the HGMA protein, for atotal of from 15 to 18 AT basepairs. In some embodiments, the AT-sDNAaptamer may have 10-12 AT basepairs. In some embodiments, the AT-sDNAaptamer has 18 AT basepairs. In some embodiments, the AT-sDNA aptamerhas 18 AT basepairs. While it is not necessary to practice theinvention, it is preferable if the AT basepairs which bind to each ofthe AT-hook binding site on the HGMA protein are consecutive.

It should also be appreciated that the sequence or sequences of theAT-sDNA aptamers which bind to each of the AT-hook binding site on theHGMA protein can be comprised entirely of adenine, entirely of thymine,or of a mixture of the two. In one embodiment of the present invention,the AT-sDNA aptamer has the nucleotide sequence,5′-G*G*G*A*A*A*A*A*A*T*T*T*T*T*T*A*A*A*A*A*A*C*C*C-3′ (SEQ ID NO: 1)where each “*” is a phosphorothioate linkage. In some embodiments, theAT-sDNA aptamer may be a 21 base oligonucleotide having the nucleotidesequence 5′-C*C*C*A*A*A*A*A*A*A*A*A*A*A*A*A*A*A*C*C*C-3′ (SEQ ID NO: 2)where each “*” is a phosphorothioate linkage. In some embodiments, theAT-sDNA aptamer may be a 21 base oligonucleotide having the nucleotidesequence 5′-G*G*G*T*T*T*T*T*T*T*T*T*T*T*T*T*T*T*G*G*G-3′ (SEQ ID NO: 3)where each “*” is a phosphorothioate linkage. In some embodiments, theAT-sDNA aptamer may be a 21 base oligonucleotide having the nucleotidesequence composed of any mixture of A and T nucleotides where thelinkage between each nucleotide is a phosphorothioate linkage.

The AT-sDNA aptamers of the present invention should have a long halflife against endogenous nuclease activity and to that end the aptamersof the present invention are made from sDNA and have phosphorothioatelinkages between all of their nucleotides. It has been found that HGMAwill bind sDNA with a similar affinity compared to normal DNA. It hasalso been found that the presence of non AT-rich DNA did not interferewith HMGA binding to AT-rich DNA.

AT-sDNA aptamers consistent with various embodiments of the presentinvention may be synthesized by any method known in the art. Suitableaptamers may be custom synthesized by a variety of commercial vendors,including by way of example, Integrated DNA Technologies of Coralville,Iowa (USA).

Further, while the AT-sDNA aptamers of the present invention has beendiscussed in terms of a single strand so that the invention may be moreeasily understood, it should be appreciated that the AT-sDNA aptamers ofthe present invention are double stranded and have a sulfur substitutionin every linkage.

As one of ordinary skill in the art will appreciate, the single strandedAT-sDNA aptamer discussed above must be annealed with a complementaryoligonucleotide strand to form the biologically active double-strandedAT-sDNA aptamers of the present invention. In some embodiments, theaptamer nucleotide sequence is self-complementary and only requiresannealing to form the duplex form. In some embodiments, the aptamersequence is not self-complementary, and in this case two distinctcomplementary sequences must be annealed to form the active duplex formof the aptamer. The complementary oligonucleotide strands may besynthesized by any method known in the art and are commerciallyavailable from a variety of vendors, including Integrated DNATechnologies of Coralville, Iowa (USA). In one embodiment, theoligonucleotide strands are annealed by combining stoichiometric amountsof each strand in a standard buffer and raising the temperature abovethe calculated melting temperature of the oligomers and letting thetemperature slowly decrease to room temperature. After annealing, theAT-sDNA aptamer may be purified using gel filtration. In one embodimentthe AT-sDNA aptamer may be purified by application onto a hydrophobicSep-Pack column with elution for desalting if necessary. In oneembodiment of the invention, the AT-sDNA aptamer is purified with aSephadex G-25 column (GE Healthcare) in H2O.

The AT-sDNA aptamer may then be transfected into a cell by any knownmeans. In one embodiment of the invention the AT-sDNA may be transfectedinto human pancreatic adenocarcinoma cells using Lipofectamine 2000,which is commercially available from Invitrogen™ (Life TechnologiesCorporation, Carlsbad, Calif. (USA)) used according to themanufacturer's protocol.

In some embodiments of the present invention, the AT-sDNA aptamer may betransfected into human cells in vivo by means of nanoparticle-aptamerbioconjugates. Suitable nanoparticle-aptamer bioconjugates are known inthe art and may be created by any known means, including those meansidentified in Farokhzad O C, Karp J M, Langer R. Nanoparticle-aptamerbioconjugates for cancer targeting. Expert Opin Drug Deliv. 2006;3:311-324. [PubMed: 16640493]; Levy-Nissenbaum E, Radovic-Moreno A F,Wang A Z, Langer R, Farokhzad O C. Nanotechnology and aptamers:applications in drug delivery. Trends Biotechnol. 2008; 26:442-449.[PubMed: 18571753]; and Lee J H, Yigit M V, Mazumdar D, Lu Y. Moleculardiagnostic and drug delivery agents based on aptamer-nanomaterialconjugates. Adv Drug Deliv Rev. 2010; 62:592-605. [PubMed: 20338204],the disclosures of which are incorporated herein by reference in theirentirety.

A representative preparation of bioconjugate nanoparticles for deliverymay be adapted from the manuscript of Farokhzad et al and summarized asfollows. Bioconjugate nanoparticles may be composed of controlledrelease polymer nanoparticles and aptamers prepared for targeteddelivery to prostate cancer cells. Specifically, poly(lacticacid)-block-polyethylene glycol (PEG) copolymer with a terminalcarboxylic acid functional group (PLA-PEG-COOH) was prepared. Fiftymicroliters of PLA-PEG-COOH nanoparticle or microparticle suspension(˜10 μg/μL in DNase RNase-free water) was incubated with 200 μL of 400mmol/L 1-(3-dimethylaminopropyl)-3-ethylcarbodimide hydrochloride (EDC)and 200 μL of 100 mmol/L N-hydroxysuccinimide (NHS) for 15 minutes atroom temperature with gentle stirring. The resulting NHS-activatedparticles were covalently linked to 50 μL of 3′-NH2-modified A10 PSMAaptamer (1 μg/μL in DNase RNase-free water) or 3′-NH2 and5′-FITC-modified A10 PSMA aptamer. The resulting aptamer-nanoparticlebioconjugates were washed, resuspended, and preserved in suspension formin DNase RNase-free water.

As discussed above, once the AT-sDNA aptamer is transfected into thecell, it inhibits the activity of both forms of HMGA by competitivesequestration of excess HMGA. This inhibition of HMGA1 activity has beenassociated with increased cell death or apoptosis even in the absence ofchemotherapy treatment. FIGS. 6A and 6B show an analysis of the growthof AsPC-1 cells transfected with CG-sDNA and AT-sDNA analyzed after 96 hto examine the effect of sDNA transfection on cell viability. Fourdifferent amounts of sDNA, 0.025 μg, 0.1 μg, 0.25 μg and 1.0 μg perwell, were used to transfect 1×10⁵ cells in 24-well plates. When cellswere transfected with 1.0 μg of sDNA, more than half of the cells weredead after 96 h for both AT-sDNA (57%, P<0.001) and CG-sDNA (60%,P<0.001). This result showed that 1.0 μg of sDNA transfection was highlytoxic to the cells independent of DNA sequence. Therefore, lower dosagesof sDNA were used to characterize sensitivity to DNA transfection. When0.25 μg sDNA was used for transfection, significantly lower viabilitieswere observed for both sDNA transfected cells. However, cell death wasgreater in cells transfected with AT-sDNA (44%, P<0.005) compared toCG-sDNA (16%, P<0.01). As the amount of sDNA transfected was decreasedto 0.1 μg, the difference in the cell death rates between CG-sDNA andAT-sDNA transfection became more pronounced. For CG-sDNA transfectedcells, 12% (P<0.05) cell death was observed whereas 33% (P<0.001) celldeath was observed for AT-sDNA transfected cells. Transfection with0.025 μg of sDNA had very little affect on cell growth, with only a 15%(P<0.05) decrease in viability for AT-sDNA transfected cells was foundwhereas the reduction in CG-sDNA transfected cells was not statisticallysignificant compared to non-transfected cells, 4% (P>0.05). Only 0.25 μgand 0.1 μg sDNA treatments showed statistically significant differencesbetween AT-sDNA and CG-sDNA transfected cells, P=0.007 and P=0.004respectively. These results indicated that inhibition of HMGA1 activityallowed for increased cell death or apoptosis, even in the absence ofchemotherapy treatment.

Furthermore, elevated HMGA protein expression in pancreatic cancer cellshas been correlated with resistance to the chemotherapy agentgemcitabine, which is commonly used in combating pancreatic cancer aswell as non-small cell lung cancer, bladder cancer and breast cancer.Use of the AT-sDNA aptamer in conjunction with standard chemotherapytreatments using gemcitabine may restore gemcitabine sensitivity bypreventing excess HMGA1 from binding to chromosomal DNA transcriptionfactors and other proteins involved in regulating apoptosis and cellproliferation in tumor progression. The HMGA-targeted AT-sDNA aptamer'sinhibition of HMGA may also result in the rescue of cellular apoptosisinduced by the gemcitabine treatment. Since these HMGA-targeted sDNAaptamers have no direct effect on HMGA gene expression levels, do notbind directly to genomic DNA and should not stimulate immunogenicresponses, HMGA-targeted AT-sDNA aptamer treatment, potentially inlocalized combination therapy with gemcitabine, may render cancer cellsmore sensitive to existing chemotherapy reagents and result in fewerside effects.

As discussed above, by virtue of their phosphorothioate linkages,AT-sDNA aptamers show significant the endogenous nuclease resistance. Insome embodiment of the invention, the AT-sDNA aptamers show significantresistance to the endogenous commercially available nucleaseDeoxyribonuclease I (Fermentas Life Sciences).

Another aspect of the invention is a method for suppressing the activityof High Mobility Group A (HMGA) proteins in human pancreatic cancercells comprising: (1) administering a therapeutically effective amountof a chemotherapy agent to a patient; and (2) administering atherapeutically effective amount of the phosphorothioate substitutedsDNA aptamer of the present invention to the patient. As used herein, achemotherapy agent is any cytotoxic antineoplastic agent thatselectively targets rapidly dividing cells such as cancer cells. Methodsof administration and therapeutically effective dosages for chemotherapyagents are well known in the art and those of ordinary skill in the artwill be able to determine a suitable method of administration andtherapeutically effective dosage amount without undue experimentation.In some embodiments, the chemotherapy agent may be gemcitabine. In someembodiments, the human cancer cells may be in human pancreatic cancercells. The sDNA aptamer may be administered to the patient using anymethod known in the art for that purpose. In some embodiments, theAT-sDNA aptamer may be transfected into human cells in vivo by means ofnanoparticle-aptamer bioconjugates.

Another aspect of the present invention is a method for increasingsensitivity to gemcitabine chemotherapy in human pancreatic cancer cellscomprising (1) administering a therapeutically effective amount ofgemcitabine, or a pharmaceutically acceptable salt thereof, to apatient; and (2) administering a therapeutically effective amount of thephosphorothioate substituted sDNA aptamer of the present invention tothe patient. In some embodiments, the AT-sDNA aptamer may be transfectedinto human cells in vivo by means of nanoparticle-aptamer bioconjugates.

Yet another aspect of the invention is a method for treating humanpancreatic adenocarcinoma comprising (1) administering a therapeuticallyeffective amount of gemcitabine, or a pharmaceutically acceptable saltthereof, to a patient; and (2) administering a therapeutically effectiveamount of the phosphorothioate substituted sDNA aptamer of the presentinvention to the patient. In some embodiments, the AT-sDNA aptamer maybe transfected into human cells in vivo by means of nanoparticle-aptamerbioconjugates, as discussed above.

In light of the foregoing, it should be appreciated that the presentinvention significantly advances the art by providing a novel andimproved pancreatic cancer therapy using an HGMA-targetedphosphorothioate DNA aptamer. While particular embodiments of theinvention have been disclosed in detail herein, it should be appreciatedthat the invention is not limited thereto or thereby inasmuch asvariations on the invention herein will be readily appreciated by thoseof ordinary skill in the art. The scope of the invention shall beappreciated from the claims that follow.

EXAMPLES

The following examples are offered to more fully illustrate theinvention, but are not to be construed as limiting the scope thereof.Further, while some of examples may include conclusions about the waythe invention may function, the inventor do not intend to be bound bythose conclusions, but put them forth only as possible explanations.Moreover, unless noted by use of past tense, presentation of an exampledoes not imply that an experiment or procedure was, or was not,conducted, or that results were, or were not actually obtained. Effortshave been made to ensure accuracy with respect to numbers used (e.g.,amounts, temperature), but some experimental errors and deviations maybe present. Unless indicated otherwise, parts are parts by weight,molecular weight is weight average molecular weight, temperature is indegrees Centigrade, and pressure is at or near atmospheric.

The methods and compositions described herein utilize or are producedusing laboratory techniques well known to skilled artisans and can befound in laboratory manuals such as Sambrook, J., et al., MolecularCloning: A Laboratory Manual, 3rd ed. Cold Spring Harbor LaboratoryPress, Cold Spring Harbor, N.Y., 2001; Spector, D. L. et al., Cells: ALaboratory Manual, Cold Spring Harbor Laboratory Press, Cold SpringHarbor, N.Y., 1998; Harlow, E., Using Antibodies: A Laboratory Manual,Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y., 1999, andAusubel, F. M., et al., ed., Current Protocols in Molecular Biology. Forpharmaceutical compositions and methods of treatment disclosed herein,dosage forms and administration regimes can be determined using standardmethods known to skilled artisans, for example as set forth in standardreferences such as Remington: the Science and Practice of Pharmacy(Alfonso R. Gennaro ed. 19th ed. 1995); Hardman, J. G., et al., Goodman& Gilman's The Pharmacological Basis of Therapeutics, Ninth Edition,McGraw-Hill, 1996; and Rowe, R. C., et al., Handbook of PharmaceuticalExcipients, Fourth Edition, Pharmaceutical Press, 2003. Organicsyntheses including synthesis of radiolabelled organic compounds can beperformed using methods and principles well known to skilled artisans,such as those set forth in standard texts such as Hedrickson et al.,Organic Chemistry 3rd edition, McGraw Hill, New York, 1970; Carruthers,W., and Coldham, I., Modern Methods of Organic Synthesis (4th Edition),Cambridge University Press, Cambridge, U.K., 2004; Curati, W. L.,Imaging in Oncology, Cambridge University Press, Cambridge, U.K., 1998;Welch, M. J., and Redvanly, C. S., eds. Handbook ofRadiopharmaceuticals: Radiochemistry and Applications, J. Wiley, NewYork, 2003.

Materials and Methods

The above compounds and others disclosed herein can be obtained, madeand tested for activity using the following procedures.

Expression and Purification of HMGA1 Protein

The cDNA for full length HMGA1b was cloned into pET-30b andover-expressed in Eschericia coli (E. Coli) BL21 (DE3). E. coliexpressing HMGA1b was cultured at 37° C. to an OD₆₀₀ measurement of 0.8to 1.0 OD₆₀₀. Protein expression was induced by the addition of 1 mMIPTG and shaking at 37° C. for 4-6 hours. HMGA1 was purified bytrichloroacetic acid precipitation as described in R. Reeves, HMGAproteins: isolation, biochemical modifications, and nucleosomeinteractions. Methods in enzymology 375 (2004) 297-322, the disclosureof which is incorporated herein by reference. Overexpressed HMGA1b wasfurther purified with a Sephadex G-25 column in H₂O and lyophilizedusing a standard freezedrying procedure. The samples were resolublizedin a 25 mM Tris-HCl (pH 6.5), 50 mM NaCl buffer for analysis.

Electrophoretic Mobility Shift Assays (EMSA)

The following 28-mer oligonucleotides were purchased from Integrated DNATechnologies (Coralville, Iowa, USA): ATf105′-(56FAM)-CGCGGGGCCGCCGCGAAAAAAAAAAACCC-3 (SEQ ID NO: 4), and ATs105′-GGGT*T*T*T*T*T*T*T*T*T*CGCGGCGGCCCCGCG-3′ (SEQ ID NO: 5) (the “*”indicates the location of phosphorothioate linkage). ATf10 contained afluorescence tag to serve as a marker for later analysis. Theseoligonucleotide samples were resuspended and annealed with complementarystrands in annealing solution (100 mM NaCl, 10 mM MgCl2 in H2O). AT10fwas annealed with its complementary strand without a fluorescence tag,and ATs10 was annealed with a strand with no sulfur substitution. Thecomplimentary strands for these oligonucleotides are commerciallyavailable and were purchased from Integrated DNA Technologies(Coralville, Iowa, USA).

CG10 5′-GGGCCCCCCCCCCCGCGGCGGCCCCGCG-3 (SEQ ID NO: 6) and Mix105′-GGGCGTGACTGAGCGCGGCGGCCCCGC G-3′ (SEQ ID NO: 7) were used as negativecontrols to demonstrate that the presence of these DNA molecules did notaffect HMGA binding to AT-rich DNA. The HMGA protein samples wereprepared in 25 mM Tris-HCl (pH 6.5), 50 mM NaCl, and the concentrationsdetermined based on UV 220 nm absorbance (ε=38,200 mol-1 cm-1). The HGMAprotein was mixed with DNA according to the ratio indicated in FIG. 1 ofJ. R. Huth, C. A. Bewley, M. S, Nissen, J. N. Evans, R. Reeves, A. M.Gronenborn, G. M. Clore, The solution structure of an HMG-I(Y)-DNAcomplex defines a new architectural minor groove binding motif. Naturestructural biology 4 (1997) 657-665, the disclosure of which isincorporated herein by reference in its entirety and incubated at 4° C.for 15 minutes prior to gel analysis. The protein-DNA complexes wereresolved on a 7.5% polyacrylmide gel and run with TAE buffer at 20 mAfor 2-3 hours at 4° C. The DNA was detected at 495 nm using theVersaDoc™ Imaging System Model 3000 from BIO-RAD Laboratories, Inc. ofHercules, Calif. (USA). The gels were further stained with coomassieblue and visualized by an AlphaImager (Alpha Innotech, San Leandro,Calif.).

Nuclease Resistance Assays

The following 21 base oligonucleotides, all containing a run of either15 consecutive adenines or thymines, were purchased from Integrated DNATechnologies, Inc. (Coralville, Iowa, USA): A155′-CCCAAAAAAAAAAAAAAACCC-3′ (SEQ ID NO: 8),T155′-GGGTTTTTTTTTTTTTTTGGG-3′ (SEQ ID NO: 9), As105′-CC*CA*AA*AA*AA*AA-*AA*AA*AA*CC*C-5′ (SEQ ID NO: 10), Ts105′-G*GG*TT*TT*TT*TT*TT*TT*TT*TG*GG-3′ (SEQ ID NO: 11), Ts205′-G*G*G*T*T*T*T*T*T*T*T*T*T*T*T*T*T*T*G*G*G-3′ (SEQ ID NO: 3), and As205′-C*C*C*A*A*A*A*A*A*A*A*A*A*A*A*A*A*A*C*C*C-3′ (SEQ ID NO: 2). Theasterisks (“*”) indicate positions of sulfur substitutions in thephosphate backbone of the nucleotide chain and the number following the“s” in the name of the oligonucleotide sequence indicates the number ofsulfur substitutions in each sequence. The samples were resuspended andannealed in an annealing solution in the following combinations: AT15(A15 and T15), As10Ts10, As10Ts20 and As20Ts20.

Each of the AT15 (A15 and T15), As10Ts10, As10Ts20 and As20Ts20combinations (0.25 nmol) was incubated with 0.5 unit ofDeoxyribonuclease I (DNaseI) (Fermentas Life Sciences) at 37° C. up to12 hours. As used herein, one unit of Deoxyribonuclease I is the amountnecessary to completely degrade 1 μg of plasmid DNA in 10 min. at 37° C.The samples were resolved on a 7% polyacrylmide gel and run with TAEbuffer at 401DA for 1-2 hours at 4° C. The gels were stained withethidium bromide and visualized by an AlphaImager (Alpha Innotech, SanLeandro, Calif.).

Cell Cultures

Human pancreatic adenocarcinoma cell lines, Panc-1, Miapaca-2 andAsPC-1, were obtained from the American Type Culture Collection(Manassas, Va.). Miapaca-2 and Panc-1 cells were grown in high glucoseDMEM medium supplemented with 10% fetal bovine serum (FBS) purchasedfrom Gibco-Life Technologies and 1% penicillin-streptomycin obtainedfrom Sigma-Aldrich. Cells were maintained in 5% CO₂ humidifiedatmosphere at 37° C. AsPC-1 cells were grown in Roswell Park MemorialInstitute medium supplemented with 10% FBS, and 1%penicillin-streptomycin. Cells were maintained in 5% CO₂ humidifiedatmosphere at 37° C. Confluent cells were trypsinized using trypsin-EDTAsolution and seeded into 100 mm dishes and maintained. When cells weregrown to 75-85% confluence in 100 mm culture dishes, the media wasaspirated and cells were trypsinized. Fresh growth media containing 10%FBS was added to the trypsinized cells (10:1 ratio) and centrifuged for5 minutes at 1,500 rpm at 4° C. After resuspending the cells in theappropriate medium, the cell count was measured using a “NeubauerCounting Chamber” hemocytometer obtained from Hauser Scientific throughFisher Scientific.

Cellular Protein Isolation and Western Blot Analysis

Cytoplasmic and nuclear protein extracts were prepared from pancreaticcancer cells using NE-PER extraction kit (Thermo Scientific, Rockford,Ill.). Protein concentrations were determined using a bicinchoninic acidassay with bovine serum albumin as a standard. Nuclear proteins thatcontained 25 or 15 μg total protein were separated by SDS-PAGE with a4%-20% Criterion gradient gel (Bio-Rad Laboratories, Inc., Hercules,Calif.). The proteins were transferred to immuno-blot PVDF membrane (0.2μm) (Bio-Rad Laboratories, Inc., Hercules, Calif.) and blocked in 5% drymilk in PBS supplemented with 0.2% Tween 20 (PBST). The PVDF membraneswere then probed with 1:1000 dilution of rabbit anti-HMGA1 antibody(Santa Cruz Biotechnology Inc, Santa Cruz, Calif.) and 1:100 dilution ofrabbit anti-HMGA2 antibody (Abcam plc, Cambridge, Mass.), in 3% BSA inPBST at 4° C. overnight. After three washes with PBST, the membrane wasblotted with secondary antibody, ant-rabbit IgG-HRP (cell signaling)1:5000 dilution in 1% dry milk in PBST at room temperature for 1 hour.An enhanced chemiluminescence detection (ECL, GE Healthcare LifeSciences, Piscataway, N.J.) system was used to detect target proteins.To ensure equal loading of the proteins between groups, membranes werere-probed with anti-TATA binding protein antibody (Abcam plc, Cambridge,Mass.).

sDNA Transfections

Cells were transfected with AT-rich phosphorothioate DNA (AT-sDNA):5′-G*G*G*A*A*A*A*A*A*T*T*T*T*T*T*A*A*A*A*A*A*C*C*C-3′ (SEQ ID NO: 1)(Integrated DNA Technologies), CG-rich phosphorothioate DNA (CG-sDNA):5′-C*C*C*C*G*G*G*C*C*C*C*G*G*C*C*G*G*G*C*G*C*C*G*C-3′ (SEQ ID NO: 12),and random phosphorothioate DNA (Mix-sDNA):5′-C*C*C*A*C*T*G*C*A*G*T*C*G*G*A*C*T*C*A*C*T*C*G*C-3′ (SEQ ID NO: 13),with the latter being used as a control that lacked a HMGA-specificbinding sequence. These oligonucleotides are available from a variety ofvendors through custom commercial synthesis. After annealing withcomplementary strands, the DNA was purified with a Sephadex G-25 column(GE Healthcare Life Sciences) in H2O. Both complementary strands alsocontained sulfur substitution at every position. Transfections usingsDNA at concentrations of 0.1 and 0.25 μg per well were conducted with5×10⁴ and 1×10⁵ Miapaca-2 and AsPC-1 cells, respectively, in 24-wellplates and all data were collected in quadruplicate. Miapaca-2 andAsPC-1 cells were transfected with sDNA using Lipofectamine 2000(Invitrogen,™ Life Technologies Corporation, Carlsbad, Calif.) accordingto the manufacturer's protocol.

Cell Growth Assays in the Presence of Gemcitabine Treatment

Cell growth was monitored using a modified crystal violet assay aspreviously described by S. Sheriff, M. Ali, A. Yahya, K. H. Haider, A.Balasubramaniam, H. Amlal, Neuropeptide Y Y5 receptor promotes cellgrowth through extracellular signal-regulated kinase signaling andcyclic AMP inhibition in a human breast cancer cell line. Molecularcancer research: MCR 8 (2010) 604-614., the disclosure of which ishereby incorporated by reference. Briefly, AsPC-1 cells grown in 10% FBScontaining RPIM medium were trypsinized using a trypsin-EDTA solutioncommercially available from the Sigma-Aldrich, and used to seed freshmedia in a 24-well plate with 105 cells per well.

Due to the shorter doubling time, 5,000 cells per well of Miapaca-2cells were seeded in a 24-well plate in 10% FBS containing DMEM medium.After 48 hours, the cells were transfected with the selected sDNA usingLipofectamine 2000 (Invitrogen,™ Life Technologies Corporation,Carlsbad, Calif.) according to the manufacturer's protocol. Thefollowing day, media was changed to fresh media containing differentconcentrations of gemcitabine (0, 1, 10, 30, 100, 1000 nM). The cellswere fixed 48 and 96 hours after gemcitabine treatment. The cells werethen fixed with 4% paraformaldehyde in PBS for 20 minutes and stained in0.1% crystal violet stain (Sigma-Aldrich) for 30 minutes. The cells werewashed under running tap water, air dried, and extracted with 0.2%Triton™ X-100 for 30 minutes. Triton™ X-100 is a widely used non-ionicsurfactant for recovery of membrane components under mild non-denaturingconditions and is commercial available from Sigma-Aldrich, among othervendors. The absorbance of the Triton X-100 was measured at 570 nm usinga HTS microplate reader. All results were analyzed for statisticalsignificance using a student's unpaired t-test. The half maximalinhibitory concentration (IC₅₀) values for gemcitabine treatment weredetermined using a Prism™ software program (Graphpad Software, SanDiego, Calif.). A p-value of <0.05 was considered statisticallysignificant.

Results EXAMPLE 1 DNA Binding Assays

In order to determine if HMGA1 DNA binding activity was affected bysulfur substitution in the DNA phosphodiester backbone, fluorescencelabeled DNA (ATf10 DNA) was used in competitive binding assays againstvarious sulfur substituted DNAs where different ratios of ATf10 DNA andATs10 DNA were added to a constant amount of purified HMGA1 (FIG. 1A).

FIG. 1A shows an image from an electrophoretic mobility shift assay(EMSA) of an HMGA1 competitive binding assay using sDNA and unmodifiedDNA. Lanes 1 and 9 are controls, ATf10 and ATs10 respectively, that donot contain HMGA1. The ratios between HMGA1 and ATf10 were kept constantat 1.5 (excess HMGA1, lane 2) and an increased amount of ATs10 was addedto the reactions in lanes 3 to 8.

The amount of free (unshifted) ATf10 DNA was determined by monitoringthe absorbance intensity at 495 nm using a BIO-RAD VersaDoc ImagingSystem Model 3000 (Bio-Rad, Hercules, Calif.) A constant ratio of ATf10DNA to HMGA1 of 1:1.5, resulted in nearly completely shifted ATf10 DNAin the absence of competitive sulfur-substituted DNA (FIG. 1A, lane2).As the ratio of ATs10 DNA to ATf10 DNA increased, the intensity of thefree ATf10 DNA band increased (FIG. 1A, lanes 2-8), indicating that theATs10 DNA was effectively competing for HMGA1 binding. Since ATs10 DNAhas no fluorescence label, no signal could be detected when onlyATs10DNA was added to HMGA1 (FIG. 1A, lane 9). At a 1:1 ratio of ATf10DNA to ATs10 DNA, approximately half of the ATf10 DNA was detected inthe unshifted position (FIG. 1A, lane 4) indicating that HMGA1 was ableto bind ATs10 DNA with a similar affinity compared to normal DNA.

Thus, the following experiments were conducted under the assumption thatHMGA1 bound sDNA with a similar affinity compared to normal DNA.

In order to demonstrate preferential HMGA binding to AT-rich DNAcompared to CG-rich or mixed sequence DNA lacking AT tracks, gel shiftassays were conducted using two controls, CG10 and Mix10. The results ofthe gel shift assays are reported on FIG. 1B. FIG. 1B shows an imagefrom the EMSA of HMGA1 competitive binding assay using CG10 and Mix10DNA. Lanes 2-4 contain equal amounts of ATf10 and CG10 or Mix10. ATf10DNA: HMGA1 in lanes 2-4 was kept constant at a 1:1 ratio. The arrowindicates free (unshifted) DNA and the “*” indicates the complex(shifted bands) with ATf10 DNA. The images were taken at 495 nm using aBIO-RAD VersaDoc Imaging System Model 3000 in order to visualize theATf10.

The CG10 sequence only contained a mixture of C and G, and the Mix10sequence contained a random sequence of A, T, C, G with no AT-stretch.The formation of an HMGA/ATf10 DNA complex (FIG. 1B, lane 2*) was stillobserved when CG10 or Mix10 DNA was present (FIG. 1B, lanes 3 and 4).

These results not only demonstrated the preference of HMGA for bindingAT-rich DNA, but also demonstrated that the presence of non AT-rich DNAdid not interfere with HMGA binding to AT-rich DNA.

EXAMPLE 2 Nuclease Resistance Assays

In order to have any potential clinical value, DNA-based aptamerstargeting HMGA1 must have a long half-life against endogenous nucleaseactivity. To explore how nuclease resistance was affected by sulfursubstitution in the HMGA1 DNA aptamers, sDNAs containing differentnumbers and positions of sulfur substitutions were subjected to nucleaseresistance assays. FIG. 2 shows an image from the nuclease resistanceassay for sDNA with DNase I. 0.25 nmol of: A) AT15; B) As10Ts10; C)As10Ts20; and D) As20Ts20 were incubated for 0 to 12 hours and run on a7% native polyacrylamide gel. The gel was stained with ethidium bromideand visualized using an AlphaImager.

The sDNA stability and nuclease activity was confirmed prior toexperiments by polyacrylamide gel electrophoresis of the sDNA andenzymatic assays confirming the activity of the nuclease. No DNA wasdetected after 30 minutes incubation when DNA with no sulfursubstitutions or with sulfur substitutions in alternate nucleotidepositions was used (FIG. 2, lanes A and B). The majority of DNAcontaining one strand with alternating sulfur substitution and the otherstrand with contiguous sulfur substitution was digested after 6 hours(FIG. 2, lane C). Only DNA with complete and contiguous sulfursubstitutions on both strands remained undigested after 12 hours ofincubation with DNaseI (FIG. 2, lane D).

EXAMPLE 3 HMGA1 Expression Levels in Pancreatic Cancer Cell Lines

HMGA1 expression in three human pancreatic cancer cell lines, AsPC-1,Miapaca-2 and Panc-1, was examined by Western blot analysis. The resultsof a western blot analysis of A) HMGA1 and B) HMGA2 expression levels inpancreatic cancer cell lines are shown on FIGS. 3A-B and 4A-B,respectively. In the assays shown in FIGS. 3A-B and 4A-B, nuclearextracts of AsPC-1, Miapaca-2, and Panc-1 cell lines were run on a 4-12%gradient gel. In each lane, 25 μg of total nuclear protein was loaded.

FIGS. 5A-B reflects the results of the western blot analysis measuringHMGA1 expression levels after transfection with CG-sDNA or AT-sDNA andin the presence of gemcitabine. 15 μg of total nuclear protein wasloaded in each lane after AsPC-1 cells treated with 100 nM gemcitabinefor 48 hours and transfected with 0.5 μg of CG-sDNA, or AT-sDNA in sixwell plates for 48 hours. The control was nuclear extract from untreatedcells.

Triplicates of each sample were run on the gel and analyzed with theAlpha Imager. The relative HMGA1 densities were obtained by dividingHMGA density by TBP density. The values were analyzed pair wise using astudent t-test, with p values <0.05 considered a significant change(*p<0.05). TATA binding protein (TBP) was used as a loading control.

AsPC-1 had the highest HMGA1 expression compared to Miapaca-2 and Panc-1(FIGS. 3A-B). The expression levels of HMGA2 are shown in FIG. 4A-B.While AsPC-1 express both HMGA1 and HMGA2, no HMGA2 protein expressionwas detected in Miapaca-2 cells. AsPC-1 cells treated with 100 nMgemcitabine exhibited no change in HMGA1 expression levels (FIGS. 5A-B).

This experiment was conducted to ensure that transfection of the aptameror gemcitabine into the cancer cells would not change the HMGA1 proteinexpression levels in the cells. HMGA1 expression levels were examinedafter transfection with CG-sDNA or AT-sDNA to determine if thetransfection procedure affected HMGA1 expression levels. The AT-sDNAused for transfection contained an 18 adenine/thymine stretch enablingHMGA1 to bind the DNA with all three AT-hooks. As a negative control, anon-HMGA1-targeted sDNA containing an equal length of DNA but with noAT-stretches, i.e. CG-sDNA, was used. Western blot analyses indicated nochanges in HMGA1 expression levels after AT-sDNA or CG-sDNA transfection(FIGS. 5A-B). We also tested transfection of the cells with 100 nMgemcitabine and observed no change in HMGA expression levels.

EXAMPLE 4 Effect of sDNA on Cell Growth

The dependence of Miapaca-2 and AsPC-1 cell viability on transfectionwith Mix-sDNA, CG-sDNA and AT-sDNA was assessed after 48 and 96 hours.The results of this assay are shown on FIGS. 6A and 6B and reported onTable 1 below. After sDNA transfection with two doses of sDNA, Miapaca-2(FIG. 6A) and AsPC-1 (FIG. 6B) cells were fixed 48 and 96 hours andanalyzed with the crystal violet assay as described in the Material andMethods section above. The absorbance was measured at 570 nm inquadruplicate. All data from control cells were combined and averaged.The values were analyzed pair wise with transfection control (TC) cellsusing a student t-test, with p values <0.05 considered a significantchange (*p<0.05, **p<0.01).

The effect of transfection alone on cell viability was assessed toestablish a transfection control (TC) baseline for comparison withcombinations of sDNA transfections and gemcitabine treatment. The TCcells were transfected with Lipofectamine 200 carrying only a vehicleand cell growth was compared to the untransfected (UT) control cells(FIGS. 6A, 6B).

In Miapaca-2, TC cells showed a 37.7% (p<0.005) and 37.6% (p<0.01)decrease in cell growth compared to UT cells after 48 and 96 hours,respectively (FIG. 6A), whereas in AsPC-1, TC cells showed 25.3%(p<0.005) and 7.9% (p>0.05) decrease in cell growth after 48 and 96hours, respectively, compared to UT cells (FIG. 6B). Similar decreasesin cell growth were observed after 0.1 ug of transfection with two sDNAcontrols, Mix-sDNA and CG-sDNA (FIGS. 6A, 6B). Specifically, in AsPC-1cells, 28.0% (p<0.005) and 33.8% (p<0.0005) of cells were dead withMix-sDNA and CG-sDNA transfection after 48 hrs, and 19.4% (p<0.01) and14.3% (p<0.05) of cells were dead after 96 hrs, respectively. InMiapaca-2, 30.4% (p<0.001) and 36.3% (p<0.005) of cells were dead withMix-sDNA and CG-sDNA transfection after 48 hrs, and 33.3% (p<0.01) and32.0% (p<0.001) of cells were dead after 96 hrs, respectively. (FIGS.6A, 6B)

These results showed that both transfection with non-AT rich sDNA and TCcells had significantly decreased cell viability compared to UT controlcells. However, comparisons between TC cells and cells transfected withMix-sDNA, and CG-sDNA showed no significant differences between thesetreatments (p>0.05) at both 48 and 96 hours. (FIGS. 6A, 6B)

When cells were transfected with AT-sDNA, however, significant decreasesin cell viability were observed compared to UT and TC controls. InMiapaca-2, 48.4% (p<0.005) and 17.2% (p<0.05) of the cells were deadafter 48 hrs compared to UT and TC controls, respectively, and after 96hrs, 58.9% (p<0.001) and 34.1% (p<0.01) of cells were dead,respectively. In AsPC-1 cells, 42.0% (p<0.005) and 22.3% (p<0.05) ofcells were dead compared to UT and TC controls after 48 hrs, and 36.1%(p<0.001) and 30.7% (p<0.01) of cells were dead after 96 hrs,respectively.

The effect of sDNA transfection dose was also examined using AsPC-1cells. Cells were transfected with four different CG-sDNA and AT-sDNAdoses, 0.025, 0.1, 0.25 and 1 μg, and cell growth compared to TC cellsat 48 (FIG. 7A) and 96 hours (FIG. 7B). When cells were transfected with1.0 μg of sDNA, more than half of the cells were dead after 96 hours forboth AT-sDNA (53.6%, p<0.0005) and CG-sDNA (56.4%, p<0.001). This resultshowed that 1.0 of sDNA transfection was highly toxic to the cellsindependent of DNA sequence. Therefore, lower dosages of sDNA were usedto characterize sensitivity to DNA transfection. When 0.25 μg sDNA wasused for transfection, both cells lines were more viable compared to the1.0 μg sDNA transfected cells, however, cell death was greater in cellstransfected with AT-sDNA (39.4%, p<0.01) compared to CG-sDNA (9.0%,p<0.05).

As the amount of sDNA transfected was decreased to 0.1 μg, the celldeath rates for the two cell lines transfected with CG-sDNA and AT-sDNAwere similar to 0.25 μg transfection; 9.7% (p<0.05) CG-sDNA, and 30.7%(p<0.01) AT-sDNA. FIGS. 7A, 7B. Transfection with 0.025 μg of sDNA hadvery little affect on cell growth, with only an 8.5% (p<0.05) decreasein viability observed for AT-sDNA transfected cells whereas thereduction in CG-sDNA transfected cells was not statistically significantcompared to TC cells (p>0.05). The 0.25 μg and 0.1 μg sDNA treatments,however, showed statistically significant differences between AT-sDNAand CG-sDNA transfected cells with p=0.007 and p=0.047, respectively.FIGS. 7A, 7B.

These results indicated that inhibition of HMGA1 activity causedincreased cell death or apoptosis even in the absence of chemotherapytreatment.

EXAMPLE 5 Gemcitabine Treatment and Cell Growth in the Presence of sDNAAptamers

Cells transfected with 0.1 or 0.25 μg of sDNA were treated with sixdifferent concentrations of gemcitabine: 0, 1, 10, 30, 100, 1000 nM.Cells were fixed after 96 hours and numbers of viable cells counted bymeasuring the absorbance at 570 nm. IC₅₀ values calculated based uponthe concentration of either gemcitabine or sDNA at which only half thecell growth is observed compared to the control experiment in absence ofgemcitabine or sDNA. FIGS. 8A-D and Table 1 report the IC₅₀determinations for the various doses of sDNA transfection withgemcitabine treatment: 0.1 μg transfection for AsPC-1 (FIG. 8A); 0.25 μgtransfection for AsPC-1 (FIG. 8B); 0.1 μg transfection for Miapaca-2(FIG. 8C); and, 0.25 μg transfection for Miapaca-2 (FIG. 8D).

TABLE 1 Fold changes in numbers of viable cells between UT andtransfected cells 96 h after transfection. Fold changes in numbers ofviable cells between TC and sDNA transfected cells 96 h aftertransfection are indicated in the parentheses. UT TC Mix CG AT Miapaca-2(0.1 μg) 1.00 −1.55 −1.45 (1.07) −1.43 (1.09)  −2.36 (−1.52) (1.00)Miapaca-2 (0.25 μg) 1.00 −1.65 −2.15 (−1.30) −6.07 (−3.68) (1.00) AsPC-1(0.1 μg) 1.00 −1.09 −1.24 (−1.14) −1.20 (−1.11) −1.57 (−1.44) (1.00)AsPC-1 (0.25 μg) 1.00 −1.09 −1.19 (−1.10) −1.79 (−1.65) (1.00)

Significant decreases in gemcitabine IC₅₀ values were observed in AsPC-1cells with AT-sDNA treatment (FIGS. 8A and 8B, Table 2). For example, at0.1 and 0.25 μg AT-sDNA treatments, IC₅₀ values were 3.8+0.2 nM and1.8+0.13 nM, respectively compared to TC values of 27.98+1.4 nM and24.8+1.45 nM, respectively.

TABLE 2 Gemcitabine IC₅₀ values of AsPC-1 and Miapaca-2 cells after0.025, 0.1 and 0.25 μg sDNA transfections. IC₅₀ values (nM) Cell lineTransfection 0.025 μg 0.1 μg 0.25 μg AsPC-1 TC 27.98 ± 1.4   24.8 ± 1.45Mix-sDNA 69.4 ± 1.1 CG-sDNA 171.53 ± 26.6 24.2 ± 2.2 46.5 ± 1.6 AT-sDNA107.49 ± 39.6  3.8 ± 0.2  1.8 ± .13 Miapaca-2 TC 11.91 ± 1.2  21.5 ± 0.6Mix-sDNA 20.43 ± 1.25 CG-sDNA 15.11 ± 1.30 21.4 ± 1.3 AT-sDNA 13.63 ±1.52 21.6 ± 1.3

The IC₅₀ values for the AT-sDNA treatments were also substantiallysmaller compared to the two control sDNA transfections with the Mix-sDNAhaving values of 69.4+1.1 nM for 0.1 μg, and the CG-sDNA having valuesof 24.2+2.2 nM and 46.5+1.6 nM, respectively. (See Table 2) Theseresults indicated that AspC-1 cells transfected with AT-sDNA were moresensitive to gemcitabine chemotherapy treatment compared to cells thatdid not receive this treatment.

On the other hand, no significant changes in IC₅₀ values were found inMiapaca-2 cells (FIGS. 8C and 8D). However, there was a significantoverall drop (˜10-fold, Table 3) in the number of viable Miapaca-2 cellsafter either 0.1 or 0.25 μg AT-sDNA transfection at doses of 100 nm orgreater gemcitabine. While the AsPC-1 cells experienced a significantdrop in gemcitabine IC₅₀, the overall drop in the number of viable cellsafter gemcitabine treatment was considerably smaller (2-4 fold) comparedto that observed for Miapaca-2 cells (Table 3).

These results indicated that cell death due to AT-sDNA transfection wassubstantially greater in Miapaca-2 cells compared to AsPC-1 cells. Theincreased cell death due to AT-sDNA transfection in comparison tocontrols (Table 1) presumably was a result of inhibition of HMGAproteins. The greater sensitivity of Miapaca-2 cells to AT-sDNA comparedto AsPC-1 cells probably has to do with the fact that Miapaca-2 cellsonly express HMGA1 whereas AsPC-1 cells express both HMGA1 and HMGA2.Therefore, the effective dose of AT-sDNA towards HMGA proteins is higherto Miapaca-2 cells in comparison to AsPC-1 cells. Neither cell linetreated with gemcitabine for 48 hours showed a dose dependent response(FIG. 9A-B). This was probably due to the fact that the cell doublingtimes of both Miapaca-2 and AsPC-1 cells are longer than 48 hours.

After 96 hours of gemcitabine treatment, Miapaca-2 cells showedincreased dose dependent responses at 0.1 μg AT-sDNA transfectioncompared to AsPC-1 cells at either 0.1 μg or 0.25 μg AT-sDNAtransfections (FIGS. 10A-D, 11A-D, 12A-C; Table 3). FIGS. 10A-D reportsa dose dependent response to gemcitabine treatment after sDNAtransfection in Miapaca-2 at 96 hours. Cells were transfected with 0.1μg of TC-sDNA, Mix-sDNA, CG-sDNA, and AT-sDNA. FIGS. 11A-D and 12A-Creport dose dependent responses to gemcitabine treatment in AsPC-1 at 96hours and 0.1 μg (FIGS. 11A-D), and 0.25 μg (FIGS. 12A-C) transfection.The data was normalized with the 0 nM gemcitabine treated cells and theresulting value defined as a value of 1. The values were analyzed inpairs using a student t-test, with p values <0.05 considered asignificant change (*p<0.05, **p<0.01, ***p<0.001).

Responses to various concentrations of gemcitabine were similar amongthe three controls, TC, Mix and CG. (FIGS. 7A-B) A significant increasein sensitivity to 10 nM gemcitabine was observed in Miapaca-2 cellstransfected with AT-sDNA with only 51.2% (p<0.05) of cells survivingcompared to 77.1% (p<0.05) in TC, 94.5% (p>0.05) in Mix-sDNA, and 83.9%(p>0.05) in CG-sDNA. In addition, at 1 nM gemcitabine treatment, 33.6%(p<0.05), cells were dead with AT-sDNA transfection whereas nosignificant change in cell viabilities were observed in TC, Mix-sDNA,and CG-sDNA transfected cells. At higher gemcitabine treatments, 30, 100and 1000 nM, significant decreases in cell viabilities were found in allthe transfected cells (9.6-35.2%, p<0.001) after 96 hours.

AsPC-1 cell sensitivity to gemcitabine treatment was assayed for 0.1 and0.25 μg sDNA transfection doses at six different gemcitabineconcentrations (FIGS. 9A-B; Table 3). Within the AT-sDNA transfectionset of experiments, the dose dependent responses to gemcitabine werestronger at the 0.25 μg transfection compared to the 0.1 μgtransfection. For example, 14.9% (p<0.05) and 41.7% (p<0.05) of thecells died in the 0.25 μg AT-sDNA transfections at 1 and 100 nMgemcitabine doses, respectively, compared to 9.0% (p>0.05) and 29.4%(p<0.05) of cells dying at 1 and 100 nM gemcitabine treatments with 0.1μg AT-sDNA transfection, respectively. At the lowest AT-sDNAtransfection dose of 0.025 μg, an insignificant effect on cell viabilitywas observed with only 8.5% cell death (p>0.05) in the absencegemcitabine treatment (FIG. 6B), whereas cell death increasedsignificantly to 31% (p<0.05) when 1000 nM gemcitabine treatment wasadministered (FIGS. 10A-D, 11A-D, 12A-C).

TABLE 3 Fold changes in numbers of viable cells normalized relative toTC for various sDNA transfections as a function of gemcitabinetreatment. sDNA used for Gemcitabine (nM) transfection 0 1 10 30 1001000 Miapaca-2 TC 1.00 1.00 −1.30 −3.21 −3.59 −3.47 (0.1 ug) Mix 1.071.12 1.01 −2.65 −4.41 −4.48 CG 1.09 1.12 −1.09 −3.29 −4.06 −4.24 AT−1.52 −1.38 −1.79 −7.07 −9.58 −6.82 Miapaca-2 TC 1.00 1.00 −1.30 −3.21−3.59 −3.47 (0.25 ug) CG −1.30 −1.38 −1.37 −2.97 −5.48 −4.11 AT −3.68−4.45 −4.14 −8.32 −11.81 −11.31 AsPC-1 TC 1.00 1.14 −1.02 −1.04 −1.36−1.52 (0.1 ug) Mix −1.14 −1.06 −1.16 −1.17 −1.36 −1.59 CG −1.11 −1.09−1.18 −1.34 −1.52 −1.67 AT −1.44 −1.58 −1.71 −1.86 −2.04 −2.33 AsPC-1 TC1.00 1.14 −1.02 −1.04 −1.36 −1.52 (0.25 ug) CG −1.10 −1.10 −1.21 −1.69−1.36 −2.16

In light of the foregoing, it should be appreciated that the presentinvention significantly advances the art by providing an HGMA-targetedphosphorothioate DNA aptamers for use in suppressing carcinogenicactivity and increasing sensitivity to chemotherapy agents in humancancer cells that are structurally and functionally improved in a numberof ways. While particular embodiments of the invention have beendisclosed in detail herein, it should be appreciated that the inventionis not limited thereto or thereby inasmuch as variations on theinvention herein will be readily appreciated by those of ordinary skillin the art. The scope of the invention shall be appreciated from theclaims that follow.

What is claimed is:
 1. An sDNA aptamer for suppressing the carcinogenicactivity of High Mobility Group A (HMGA) proteins in human cells havinga nucleotide sequence comprising a segment selected from the groupconsisting of: 5′-G*G*G*A*A*A*A*A*A*T*T*T*T*T*T*A*A*A*A*A*A*-C*C*C-3′(SEQ ID NO: 1); 5′-C*C*C*A*A*A*A*A*A*A*A*A*A*A*A*A*A*A*C*C*C-3′ (SEQ IDNO: 2); 5′-G*G*G*T*T*T*T*T*T*T*T*T*T*T*T*T*T*T*G*G*G-3′ (SEQ ID NO: 3);5′-GGGT*T*T*T*T*T*T*T*T*T*CGCGGCGGCCCCGCG-3′ (SEQ ID NO: 5);5′-CC*CA*AA*AA*AA*AA*AA*AA*AA*CC*C-5′ (SEQ ID NO: 10), and5′-G*GG*TT*TT*TT*TT*TT*TT*TT*TG*GG-3′ (SEQ ID NO: 11); wherein arephosphorothioate linkages.
 2. The sDNA aptamer of claim 1 wherein thelength of the sDNA aptamer is from about 17 to about 30 base pairs. 3.The sDNA aptamer of claim 1 having the sequence5′-G*G*G*A*A*A*A*A*A*T*T*T*T*T*T*A*A*A*A*A*A*C*C*C-3′ (SEQ ID NO.: 1)wherein the * are phosphorothioate linkages.
 4. The sDNA aptamer ofclaim 1 wherein said sDNA aptamer can be transfected into at least onehuman cell type.
 5. The sDNA aptamer of claim 1 wherein said sDNAaptamer inhibits HMGA protein activity in human cancer cells byproviding binding sites for said HGMA proteins, thereby preventing themfrom binding to genomic DNA.
 6. The sDNA aptamer of claim 5 wherein saidhuman cancer cells are human pancreatic adenocarcinoma cells.
 7. ThesDNA aptamer of claim 6 wherein said sDNA aptamer increases sensitivityof human cancer cells to gemcitabine.
 8. The sDNA aptamer of claim 7wherein said human cancer cells are human pancreatic adenocarcinomacells.
 9. The sDNA aptamer of claim 1 wherein said sDNA aptamer iscontained within a nanoparticle-aptamer bioconjugate for delivery tocells in vivo.